From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 11 2009 - 12:11:57 CDT
> Thank you for your answer. If I don't use minimization on, but only
> minimize command after few steps I have the error:
> bad global exclusion clount. Instead with minimization on the
> minimization run without errors until the end.
I can't think of any reason for minimize n and minimization on; run n to
yield different results... could you send me snippets of the end of the
relevant config files?
Bad global exclusion count errors generally indicate an overly long bond
in the system... can you visually inspect your structure and make sure
it looks ok?
By the way, is namd terminating upon the exclusion count error? During
minimization, bad global exclusion counts should give a warning but not
> if I run minimization and MD with different conf file, can I use restart
> coordinate and velocity files obtained from minimization to start MD?
> thanks again for help
Yes; you can read the coordinates, velocities, and extended system from
the previous run with bincoordinates, binvelocities, and extendedSystem,
respectively (they'll be named $outputname.restart.coor/vel/xsc)
By the way, are you sure you mean to be running without pme?
Also, that rigid bond tolerance is quite large...
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